created test suite, and created script for the reading in of information to a...

created test suite, and created script for the reading in of information to a Datapoints object, with the arrays initialised.

solventmapcreator/io/solvationenergyreader.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for the reading in of solvation energies for a given solvent.
+
+@author: mark
+"""
+
+import logging
+import resultsanalysis.fileparsing.xmlparsing.solvationreader as solvationreader
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+def parse_free_energy_from_file_with_data_arrays(filename):
+    """This reads in the information form file to a Dapoints object, and
+    creates the data arrays.
+    """
+    datapoints = parse_free_energy_from_file(filename)
+    datapoints.createDataArrays()
+    return datapoints
+
+def parse_free_energy_from_file(filename):
+    """This parses the file and returns a datapoints representation of it.
+    """
+    solvation_energy_dict = parse_free_energy_info(filename)
+    return create_datapoints_with_values(solvation_energy_dict)
+
+def create_datapoints_with_values(solvation_energy_dict):
+    """
+    """
+    return solvationreader.create_datapoints_with_values(solvation_energy_dict)
+
+def parse_free_energy_info(filename):
+    """This extracts the slvation information to a dictionary.
+    """
+    return solvationreader.parse_free_energy_info(filename)

solventmapcreator/test/iotest/solvationenergyreadertest.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script containing tests for the solvationenergyreader module.
+
+@author: mark
+"""
+
+import logging
+import unittest
+import numpy as np
+import solventmapcreator.io.solvationenergyreader as solvationenergyreader
+from resultsanalysis.dataclasses.datapoints import Datapoints
+from resultsanalysis.dataclasses.datapoint import Datapoint
+from resultsanalysis.dataclasses.units import Units
+from resultsanalysis.dataclasses.value import Value
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+class SolvationEnergyReaderTestCase(unittest.TestCase):
+    """Test Case for the solvationenergyreader module.
+    """
+    def setUp(self):
+        """Set up for tests
+        """
+        self.solvation_info_dict = solvationenergyreader.parse_free_energy_info("resources/energyvaluestest.xml")
+        self.expected_datapoints = Datapoints(("ssip",""), (Units.dimensionless, Units.kj_per_mol))
+        self.expected_datapoints.addDatapoint(Datapoint(Value(-14.100, "ssip",
+                                                              Units.dimensionless),
+                                                        Value(-34.8195308084233,
+                                                              "", Units.kj_per_mol),
+                                                              "-14.100solute"))
+    def tearDown(self):
+        """Tear down after tests.
+        """
+        del self.solvation_info_dict
+        del self.expected_datapoints
+    def test_parse_free_energy_from_file_with_data_arrays(self):
+        """Test to see if 
+        """
+        actual_datapoints = solvationenergyreader.parse_free_energy_from_file_with_data_arrays("resources/energyvaluestest.xml")
+        self.assertEqual(self.expected_datapoints, actual_datapoints)
+        np.testing.assert_array_almost_equal(np.array([[-14.100]]),
+                                             actual_datapoints.x_values)
+        np.testing.assert_array_almost_equal(np.array([[-34.8195308084233]]),
+                                             actual_datapoints.y_values)
+    def test_parse_free_energy_from_file(self):
+        """Test to see if expected Datapoints object is created from reading of
+        a file.
+        """
+        actual_datapoints = solvationenergyreader.parse_free_energy_from_file("resources/energyvaluestest.xml")
+        self.assertEqual(self.expected_datapoints, actual_datapoints)
+    def test_create_datapoints_with_values(self):
+        """Test to see if expected Datapoints object is created.
+        """
+        actual_datapoints = solvationenergyreader.create_datapoints_with_values(self.solvation_info_dict)
+        self.assertEqual(self.expected_datapoints, actual_datapoints)
+    def test_parse_free_energy_info(self):
+        """Test to see if expected free energy values are extracted from file.
+        """
+        expected_dict = {"total_energy": -34.8195308084233, "value_type":"MOLEFRACTION",
+                         "to_solvent_id":"water", "from_solvent_id":"",
+                         "stdinchikey":"-14.100solute"}
+        actual_dict_dict = solvationenergyreader.parse_free_energy_info("resources/energyvaluestest.xml")
+        self.assertListEqual(["-14.100solute"], sorted(actual_dict_dict.keys()))
+        actual_dict = actual_dict_dict["-14.100solute"]
+        self.assertListEqual(sorted(expected_dict.keys()), sorted(actual_dict.keys()))
+        for key, value in expected_dict.items():
+            if key == "total_energy":
+                self.assertAlmostEqual(value, actual_dict[key])
+            else:
+                self.assertEqual(value, actual_dict[key])
\ No newline at end of file

solventmapcreator/test/solvationmapcreatortests.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for running the tests.
+
+@author: mark
+"""
+
+import logging
+import unittest
+from solventmapcreator.test.iotest.solvationenergyreadertest import SolvationEnergyReaderTestCase
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+IO_TEST_CASES = [SolvationEnergyReaderTestCase]
+
+def test_suite():
+    """Function creates a test suite and then loads all the tests from the
+    different test cases.
+    """
+    LOGGER.info("setting up loader and test suite")
+    loader = unittest.TestLoader()
+    suite = unittest.TestSuite()
+    for test_case in IO_TEST_CASES:
+        LOGGER.debug("Adding %s", test_case)
+        suite.addTests(loader.loadTestsFromTestCase(test_case))
+    return suite
+
+if __name__ == '__main__':
+    LOGGER.info("calling test suite method")
+    SUITE = test_suite()
+    LOGGER.info("running test suite")
+    unittest.TextTestRunner(verbosity=2).run(SUITE)